Molecular evaluation of genetic diversity and association studies in rice (<Emphasis Type="BoldItalic">Oryza sativa</Emphasis> L.)

In the present study, we tested rice genotypes that included un(der)exploited landraces of Tamil Nadu along with indica and japonica test cultivars to ascertain their genetic diversity structure. Highly polymorphic microsatellite markers were used for generating marker segregation data. A novel measure, allele discrimination index, was used to determine subpopulation differentiation power of each marker. Phenotypic data were collected for yield and component traits. Pattern of molecular differentiation separated indica and japonica genotypes; indica genotypes had two subpopulations within. Landraces were found to have indica genome, but formed a separate subgroup with low linkage disequilibrium. The landraces further separated into distinct group in both hierarchical clustering analysis using neighbour-joining method as well as in the model based population structure analysis. Japonica and the remaining indica cultivars formed two other distinct groups. Linkage disequilibrium observed in the whole population was considerably reduced in subpopulations. Low linkage disequilibrium of landforms suggests their narrow adaptation in local geographical niche. Many population specific alleles could be identified particularly for japonica cultivars and landraces. Association analysis revealed nine marker-trait associations with three agronomic traits, of which 67% were previously reported. Although the testing landraces together with known cultivars had permitted genomewide association mapping, the experiment offers scope to study more landraces collected from the entire geographical region for drawing more reliable information.     

黔东南香禾糯AFLP遗传多样性分析与评价

香禾糯是我国侗族人民数百年来的传统主食,也是传统农业生态系统的重要组成部分。本文通过民族植物学调查与现代分子生物学试验相结合的方法,对黔东南侗族地区传统分类的香禾糯农家品种进行了评价,以便探讨香禾糯种质资源的遗传多样性变化。通过8对AFLP引物并基于遗传距离和遗传相似系数,对从黔东南侗族地区收集的95个香禾糯农家品种进行了分析。共检测到707个位点,其中多态性位点为619个,占87.55%,Shannon-Weiner多样性指数为0.3738,基因多样性指数为0.2446,遗传相似系数为0.7121~0.9958。当遗传相似系数为0.7546时,可划分为Ⅰ、Ⅱ两大类,外加1个特殊品种,其中Ⅰ类群有88个品种,Ⅱ类群有6个品种,来自相同和相邻侗寨或者形态性状相近的品种并没有完全聚在一起。结果表明黔东南地区香禾糯农家品种遗传多样性总体水平较高,特别是传统耕作文化保护较好的侗寨内,其遗传背景差异较大。香禾糯种质资源的多样性形成,在很大程度上与黔东南地区复杂多变的自然环境有关,还与该地区少数民族的传统耕作制度和民族传统文化延续密切相关。     

Genome-wide haplotype changes produced by artificial selection during modern rice breeding in Japan

During the last 90 years, the breeding of rice has delivered cultivars with improved agronomic and economic characteristics. Crossing of different lines and successive artificial selection of progeny based on their phenotypes have changed the chromosomal constitution of the ancestors of modern rice; however, the nature of these changes is unclear. The recent accumulation of data for genome-wide single-nucleotide polymorphisms (SNPs) in rice has allowed us to investigate the change in haplotype structure and composition. To assess the impact of these changes during modern breeding, we studied 177 Japanese rice accessions, which were categorized into three groups: landraces, improved cultivars developed from 1931 to 1974 (the early breeding phase), and improved cultivars developed from 1975 to 2005 (the late breeding phase). Phylogenetic tree and structure analysis indicated genetic differentiation between non-irrigated (upland) and irrigated (lowland) rice groups as well as genetic structuring within the irrigated rice group that corresponded to the existence of three subgroups. Pedigree analysis revealed that a limited number of landraces and cultivars was used for breeding at the beginning of the period of systematic breeding and that 11 landraces accounted for 70% of the ancestors of the modern improved cultivars. The values for linkage disequilibrium estimated from SNP alleles and the haplotype diversity determined from consecutive alleles in five-SNP windows indicated that haplotype blocks became less diverse over time as a result of the breeding process. A decrease in haplotype diversity, caused by a reduced number of polymorphisms in the haplotype blocks, was observed in several chromosomal regions. However, our results also indicate that new haplotype polymorphisms have been generated across the genome during the breeding process. These findings will facilitate our understanding of the association between particular haplotypes and desirable phenotypes in modern Japanese rice cultivars.     

Functional Genetic Diversity Analysis and Identification of Associated Simple Sequence Repeats and Amplified Fragment Length Polymorphism Markers to Drought Tolerance in Lentil (<Emphasis Type="Italic">Lens culinaris</Emphasis> ssp. <Emphasis Type="Italic">culinaris</Emphasis> Medicus) Landraces

Genetic diversity of 70 Mediterranean lentil (Lens culinaris ssp. culinaris Medicus) landraces was assessed using simple sequence repeats (SSRs) and amplified fragment length polymorphisms (AFLPs). These landraces were also assessed for variation in root and shoot traits and drought tolerance as estimated by relative water content (RWC), water losing rate (WLR) and wilting score (WS). Genetic diversity and clear differentiation of Moroccan landraces from those from northern Mediterranean regions (Italy, Turkey and Greece) were found. High genetic variation in root and shoot traits and traits related to drought tolerance was also observed. No relationship was found between drought tolerance of landraces and their geographic origin. Landraces with higher dry root biomass, chlorophyll content and root–shoot ratio were drought tolerant as evidenced by higher RWC and lower WLR and wilting severity. Kruskal–Wallis non-parametric test (K-W) was used to find SSRs and AFLPs associated with RWC, WLR and WS. Regression analysis showed six SSR and AFLP alleles explaining the highest phenotypic variation of RWC, WLR and WS (ranging from 21 to 50 % for SSRs and from 14 to 33 % for AFLPs). Functional genetic diversity analysis showed relationships between drought response of landraces and linked SSR and AFLP alleles to RWC, WLR and WS according to K-W test using canonical discriminant analysis. Our results confirm the feasibility of using association mapping to find DNA markers associated with drought tolerance in larger numbers of lentil landraces.     

Genetic diversity among cultivars, landraces and wild relatives of rice as revealed by microsatellite markers

Genetic diversity among 35 rice accessions, which included 19 landraces, 9 cultivars and 7 wild relatives, was investigated by using microsatellite (SSR) markers distributed across the rice genome. The mean number of alleles per locus was 4.86, showing 95.2% polymorphism and an average polymorphism information content of 0.707. Cluster analysis based on microsatellite allelic diversity clearly demarcated the landraces, cultivars and wild relatives into different groups. The allelic richness computed for the clusters indicated that genetic diversity was the highest among wild relatives (0.436), followed by landraces (0.356), and the lowest for cultivars. Allelic variability among the SSR markers was high enough to categorize cultivars, landraces and wild relatives of the rice germplasm, and to catalogue the genetic variability observed for future use. The results also suggested the necessity to introgress genes from landraces and wild relatives into cultivars, for cultivar improvement.     

Comparative analysis on the genetic relatedness of Sorghum bicolor accessions from Southern Africa by RAPDs,AFLPs and SSRs

In order to get an overview on the genetic relatedness of sorghum (Sorghum bicolor) landraces and cultivars grown in low-input conditions of small-scale farming systems, 46 sorghum accessions derived from Southern Africa were evaluated on the basis of amplified fragment length polymorphism (AFLPs), random amplified polymorphic DNAs (RAPDs) and simple sequence repeats (SSRs). By this approach all sorghum accessions were uniquely fingerprinted by all marker systems. Mean genetic similarity was estimated at 0.88 based on RAPDs, 0.85 using AFLPs and 0.31 based on SSRs. In addition to this, genetic distance based on SSR data was estimated at 57 according to a stepwise mutation model (Deltamu-SSR). All UPGMA-clusters showed a good fit to the similarity estimates (AFLPs: r = 0.92; RAPDs: r = 0.88; SSRs: r = 0.87; Deltamu-SSRs: r = 0.85). By UPGMA-clustering two main clusters were built on all marker systems comprising landraces on the one hand and newly developed varieties on the other hand. Further sub-groupings were not unequivocal. Genetic diversity (H, DI) was estimated on a similar level within landraces and breeding varieties. Comparing the three approaches to each other, RAPD and AFLP similarity indices were highly correlated (r = 0.81), while the Spearman's rank correlation coefficient between SSRs and AFLPs was r = 0.57 and r = 0.51 between RAPDs and SSRs. Applying a stepwise mutation model on the SSR data resulted in an intermediate correlation coefficient between Deltamu-SSRs and AFLPs (r = 0.66) and RAPDs ( r = 0.67), respectively, while SSRs and Deltamu-SSRs showed a lower correlation coefficient (r = 0.52). The highest bootstrap probabilities were found using AFLPs (56% on average) while SSR, Deltamu-SSR and RAPD-based similarity estimates had low mean bootstrap probabilities (24%, 27%, 30%, respectively). The coefficient of variation (CV) of the estimated genetic similarity decreased with an increasing number of bands and was lowest using AFLPs.     

水稻一多拷贝微卫星DNA多态性分析

用一个多拷贝微卫星 DNA标记分析了238份栽培水稻的遗传多样性及遗传多样性从农家品种到现代栽培品种的动态变化。共检测出16种长度变异类型和32种表现型,但长度变异类型数、表现型数和表现型多样性水平在农家品种和现代栽培品种间没有显著差别。该标记在遗传资源评价和DNA指纹图谱建设中有重要的应用价值,也是研究环境或人工对多拷贝基因选择作用的一个良好模型。 Abstract:The genetic diversity of 238 cultivated rice and its difference between landraces and modern cultivars have been assayed using a multiple copy microsatellite DNA marker.Although 16 length variants and 32 phenotypes were found in all accessions,no significant differences in number of length variants,number of phenotypes and phenotypic diversity were detected between landraces and modern cultivars.This marker is of great value in evaluating genetic germplasm and constructing DNA fingerprints of rice and provides an elite model for tracing effectiveness of natural and artificial selection on multiple copy genes.     

Genetic variation detected with RAPD markers among upland and lowland rice cultivars (Oryza sativa L.)

Genetic variation of nine upland and four lowland rice cultivars (Oryza sativa L.) was investigated at the DNA level using the randomly amplified polymorphic DNA (RAPD) method via the polymerase chain reaction (PCR). Forty-two random primers were used to amplify DNA segments and 260 PCR products were obtained. The results of agarosegel electrophoretic analysis of these PCR products indicated that 208 (80%) were polymorphic. All 42 primers used in this experiment were amplified and typically generated one-to-four major bands. Only two primers showed no polymorphisms. In general, a higher level of polymorphism was found between japonica and indica subspecies while fewer polymorphisms were found between upland and lowland cultivars within the indica subspecies. A dendrogram that shows the genetic distances of 13 rice cultivars was constructed based on their DNA polymorphisms. Classification of rice cultivars based on the results from the RAPD analysis was identical to the previous classification based on isozyme analysis. This study demonstrated that RAPD analysis is a useful tool in determining the genetic relationships among rice cultivars.     

Genetic Diversity and Population Structure Among Oat Cultivars and Landraces

In this study, genetic diversity among 177 oat (Avena sativa L.) accessions including both white and red oat landraces and 36 commercial cultivars was studied for simple sequence repeat (SSR) loci. Thirty-one genomic and expressed sequence tags (EST)-derived primer pairs were selected according to high polymorphism from an initial 66 SSR batch. Markers revealed a high level of polymorphism, detecting a total of 454 alleles. The average gene diversity for the whole sample was 0.29. Genetic similarity, calculated using the Dice coefficient, was used for cluster analysis, and principal component analysis was also applied. In addition, population structure using a Bayesian clustering approach identified discrete subpopulation based on allele frequency and showed similar clustering of oat genotypes in four groups. Accessions could be classified into four main clusters that clearly separated the commercial cultivars, the red oat landraces and two clusters of white oat landraces. Cultivars showed less diversity than the landraces indicating a reduction of genetic diversity during breeding, whereas white oat landraces showed higher diversity than red ones. The average polymorphic information content of 0.80 for the SSR loci indicated the usefulness of many of the SSR for genotype identification. In particular, two markers, MAMA5 and AM04, with a total of 50 alleles and a high discrimination power (>0.90), were sufficient to discriminate among all commercial cultivars studied highlighting their potential use for variety identification.     

Molecular Characterization and Comparative Analysis of Six Durum Wheat Accessions Including Graziella Ra

Genetic identity and relatedness of the durum wheat Graziella Ra, four Italian commercial durum cultivars (Cappelli, Grazia, Flaminio and Svevo) and Kamut were evaluated using amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs) and α-gliadin gene sequence analysis. Our primary objective was to study molecular genetic diversity in such a set of wheats including three modern (Grazia, Flaminio and Svevo) and three older (Cappelli, Kamut and Graziella Ra) durum accessions. Specifically, we aimed at determining the relationship between the historic accession Graziella Ra and Kamut, which is considered an ancient relative of the durum subspecies. Obtained results revealed that (1) both AFLP and SSR molecular markers detected highly congruent patterns of genetic diversity among the accessions showing nearly similar efficiency; (2) for AFLPs, percentage of polymorphic loci within accession ranged from 6.57% to 19.71% (mean, 12.77%) and for SSRs, from 0% to 57.14% (mean, 28.57%); (3) principal component analysis of genetic distance among accessions showed the first two axes accounting for 58.03% (for AFLPs) and 61.60% (for SSRs) of the total variability; (4) for AFLPs, molecular variance was partitioned into 80% (variance among accessions) and 20% (within accession) and for SSRs, into 73% (variance among accessions) and 27% (within accession); (5) cluster analysis of AFLPs and SSRs datasets displayed Graziella Ra and Kamut constantly grouped into the same cluster; and (6) molecular comparison of α-gliadin gene sequences showed Graziella Ra and Kamut in separate clusters. All these findings support the hypothesis that Graziella Ra and Kamut, although very similar, at least in the little part of the genome investigated by molecular markers employed in this study, might be considered as distinct accessions.     

Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice

Genetic polymorphisms of ten microsatellite DNA loci were examined among 238 accessions of landraces and cultivars that represent a significant portion of the distribution range for both indica and japonica groups of cultivated rice. In all, 93 alleles were identified with these ten markers. The number of alleles varied from a low of 3 or 4 at each of four loci, to an intermediate value of 9–14 at five loci, and to an extra-ordinarily high 25 at one locus. The numbers of alleles per locus are much larger than those detected using other types of markers. The number of alleles detected at a locus is significantly correlated with the number of simple sequence repeats in the targeted microsatellite DNA. Indica rice has about 14% more alleles than japonica rice, and such allele number differences are more pronounced in landraces than in cultivars. The indica-japonica differentiation component accounted for about 10% of the diversity in the total sample, and twice as much differentiation was detected in cultivars as in landraces. About two-thirds as many alleles were observed in cultivars as in landraces; another two-thirds of the alleles in the cultivar group were found in modern elite cultivars or parents of hybrid rice. The majority of the simple sequence repeat (SSR) alleles that were present in high or intermediate frequencies in landraces ultimately survived into modern elite cultivars and hybrids. The greater resolving power and the efficient production of massive amounts of SSR data may be particularly useful for germplasm assessment and evolutionary studies of crop plants.     

Diversity of North European oat analyzed by SSR, AFLP and DArT markers

Oat is an important crop in Nordic countries both for feed and human consumption. Maintaining a high level of genetic diversity is essential for both breeding and agronomy. A panel of 94 oat accessions was used in this study, including 24 museum accessions over 100- to 120-year old and 70 genebank accessions from mainly Nordic countries and Germany, covering different breeding periods. Sixty-one polymorphic SSR, 201 AFLP and 1056 DArT markers were used to evaluate the past and present genetic diversity of the Nordic gene pool. Norwegian accessions showed the highest diversity, followed by Swedish and Finnish, with German accessions the least diverse. In addition, the Nordic accessions appeared to be highly interrelated and distinct from the German, reflecting a frequent germplasm exchange and interbreeding among Nordic countries. A significant loss of diversity happened at the transition from landraces and old cultivars to modern cultivars. Modern oat originated from only a segment of the landraces and left the remainder, especially black oat, unused. However, no significant overall diversity reduction was found during modern breeding periods, although fluctuation of diversity indices was observed. The narrow genetic basis of the modern Nordic gene pool calls for increasing genetic diversity through cultivar introduction and prebreeding based on neglected sources like the Nordic black oat.     

Genetic differentiation analysis of African cassava (Manihot esculenta) landraces and elite germplasm using amplified fragment length polymorphism and simple sequence repeat markers

Molecular‐marker‐aided evaluation of germplasm plays an important role in defining the genetic diversity of plant genotypes for genetic and population improvement studies. A collection of African cassava landraces and elite cultivars was analysed for genetic diversity using 20 amplified fragment length polymorphic (AFLP) DNA primer combinations and 50 simple sequence repeat (SSR) markers. Within‐population diversity estimates obtained with both markers were correlated, showing little variation in their fixation index. The amount of within‐population variation was higher for landraces as illustrated by both markers, allowing discrimination among accessions along their geographical origins, with some overlap indicating the pattern of germplasm movement between countries. Elite cultivars were grouped in most cases in agreement with their pedigree and showed a narrow genetic variation. Both SSR and AFLP markers showed some similarity in results for the landraces, although SSR provided better genetic differentiation estimates. Genetic differentiation (Fst) in the landrace population was 0.746 for SSR and 0.656 for AFLP. The molecular variance among cultivars in both populations accounted for up to 83% of the overall variation, while 17% was found within populations. Gene diversity (H_e) estimated within each population varied with an average value of 0.607 for the landraces and 0.594 for the elite lines. Analyses of SSR data using ordination techniques identified additional cluster groups not detected by AFLP and also captured maximum variation within and between both populations. Our results indicate the importance of SSR and AFLP as efficient markers for the analysis of genetic diversity and population structure in cassava. Genetic differentiation analysis of the evaluated populations provides high prospects for identifying diverse parental combinations for the development of segregating populations for genetic studies and the introgression of desirable genes from diverse sources into the existing genetic base.     

Genetic Analysis of Indian Lentil (Lens culinaris Medikus) Cultivars and Landraces Using RAPD and STMS Markers

Molecular analysis of 29 lentil (Lens culinaris) cultivars and landraces of Indian origin was carried out using twenty RAPD and ten cross-species STMS primers. A total of 97 markers (72 RAPD and 25 STMS) were amplified of which 42.3% were polymorphic. Genetic similarity among the cultivars and landraces was 89.7%. The observed results indicated low level of genetic diversity in the studied material. UPGMA cluster analysis for the combined data of RAPD and STMS revealed two broad clusters — Cluster I with three landraces and Cluster II containing all remaining landraces and cultivars except Precoz. Germplasm line Precoz was found to be the most distinct in individual as well as combined analyses. All cultivars and landraces except K-75 and L4076 could be discriminated from one another using combined data for the two techniques. Germplasm lines Precoz, L830 and cultivars L4147 and JL3 were quite distinct and could be potential germplasm resource.     

不同SSR标记检测技术及其在花生栽培种遗传多样性分析中的应用

以85份花生栽培种为材料,分别应用银染法和荧光检测法检测9对SSR引物的扩增产物。比较结果显示,荧光检测法具有灵敏度高、检测结果准确、效率高等优点。聚类分析表明,银染法与荧光检测法分别能够区分74个、82个花生品种,并分别聚成8个、9个类群;荧光检测法的聚类结果虽然反映的品种间遗传多样性较低,但与品种类型、产地及其亲缘关系相关程度更高,表明荧光检测数据更精确、可靠。遗传多样性分析发现,地方品种的遗传多样性指数最高,其次为多粒型育成品种,表明我国地方品种和多粒型育成品种蕴藏了丰富的优异性状,有利于对其挖掘和利用。     

Unused genetic resources: a case study of Polish common oat germplasm

Landraces and old, obsolete cultivars are a rich source of diversity and could become important and easy‐to‐use germplasm resources for breeding. They are characterised by yield stability, broad adaptation, tolerance to diseases and a greater competitiveness in the presence of weeds. The main objective of this study was to estimate and compare the genetic diversity among and within landraces, old cultivars and modern cultivars of common oat. Inter simple sequence repeats were used to study the genetic diversity of 12 modern Polish cultivars, 23 old Polish cultivars, 19 native landraces and 5 contemporary European cultivars. The results indicated a low amount of diversity among Polish modern cultivars, but an even lower diversity among old Polish cultivars, as well as large differences between these two gene pools. As expected, the landraces were the most diverse group and showed the highest internal variation. The landraces and old cultivars might serve as sources of useful alleles that have never been used in breeding. Additionally, it was possible to identify errors and inconsistencies in the passport data of gene‐bank accessions. These results can be applied to the maintenance and management of gene‐bank collections.     

Genetic relationship among wild,landraces and cultivars of hazelnut (Corylus avellana) from Portugal revealed through ISSR and AFLP markers

The genus Corylus, a member of the birch family Betulaceae, includes several species that are widely distributed throughout temperate regions of the Northern Hemisphere. This study assesses the genetic diversity in 26 international cultivars and 32 accessions of Corylus avellana L. from Portugal: 13 wild genotypes and 19 landraces. The genetic relationships among the 58 hazelnuts (Corylus avellana L.) were analyzed using inter simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP) markers. Eighteen ISSR primers and seven AFLP primer pairs generated a total of 570 unambiguous and repeatable bands, respectively, from which 541 (95.03 %) were polymorphic for both markers. Genetic similarity index values ranged from 0.239 for wild types and cultivars to 0.143 for landraces and wild types. The genetic relationships were presented as a Neighbor-Joining method dendrogram and a two-dimensional principal coordinate analysis (PCoA) plot. The Neighbor-Joining dendrogram showed three main clusters, and the PCoA analysis has shown to be congruent with the hierarchical analysis. Bayesian analysis clustered all individuals into three groups showing a good separation among wild genotypes, landraces and cultivars. The genetic diversity found on wild genotypes and Portuguese landraces may provide relevant information for the diversity conservation and it will be useful in breeding programs and to identify local selections for preservation.     

Genetic diversity and phylogeny of Japanese sake-brewing rice as revealed by AFLP and nuclear and chloroplast SSR markers

Japanese rice (Oryza sativa L.) cultivars that are strictly used for the brewing of sake (Japanese rice wine) represent a unique and traditional group. These cultivars are characterized by common traits such as large grain size with low protein content and a large, central white-core structure. To understand the genetic diversity and phylogenetic characteristics of sake-brewing rice, we performed amplified fragment length polymorphism and simple sequence repeat analyses, using 95 cultivars of local and modern sake-brewing rice together with 76 cultivars of local and modern cooking rice. Our analysis of both nuclear and chloroplast genome polymorphisms showed that the genetic diversity in sake-brewing rice cultivars was much smaller than the diversity found in cooking rice cultivars. Interestingly, the genetic diversity within the modern sake-brewing cultivars was about twofold higher than the diversity within the local sake-brewing cultivars, which was in contrast to the cooking cultivars. This is most likely due to introgression of the modern cooking cultivars into the modern sake-brewing cultivars through breeding practices. Cluster analysis and chloroplast haplotype analysis suggested that the local sake-brewing cultivars originated monophyletically in the western regions of Japan. Analysis of variance tests showed that several markers were significantly associated with sake-brewing traits, particularly with the large white-core structure.     

Genetic diversity analysis of traditional and improved Indonesian rice (Oryza sativa L.) germplasm using microsatellite markers

The archipelago of Indonesia has a long history of rice production across a broad range of rice-growing environments resulting in a diverse array of local Indonesian rice varieties. Although some have been incorporated into modern breeding programs, the vast majority of these landraces remain untapped. To better understand this rich source of genetic diversity we have characterized 330 rice accessions, including 246 Indonesian landraces and 63 Indonesian improved cultivars, using 30 fluorescently-labeled microsatellite markers. The landraces were selected across 21 provinces and include representatives of the classical subpopulations of cere, bulu, and gundil rices. A total of 394 alleles were detected at the 30 simple sequence repeat loci, with an average number of 13 alleles per locus across all accessions, and an average polymorphism information content value of 0.66. Genetic diversity analysis characterized the Indonesian landraces as 68% indica and 32% tropical japonica, with an indica gene diversity of 0.53 and a tropical japonica gene diversity of 0.56, and a Fst of 0.38 between the two groups. All of the improved varieties sampled were indica, and had an average gene diversity of 0.46. A set of high quality Indonesian varieties, including Rojolele, formed a separate cluster within the tropical japonicas. This germplasm presents a valuable source of diversity for future breeding and association mapping efforts.     

Analysis of genetic variability of Fusarium oxysporum f. sp. cepae the causal agent of basal rot on onion using RAPD markers

Genetic variability among isolates of Fusarium oxysporum f. sp. cepae was obtained from different onion-growing areas of Tamil Nadu, India. Random amplified polymorphic DNA (RAPD) analysis was carried out using 12 random primers, each of them consisting of 10 base pairs. Four out of the 12 primers were differentiated between some of the tested F. oxysporum f. sp. cepae isolates. Analysis of the genetic coefficient matrix derived from the scores of RAPD profile showed that minimum and maximum per cent similarities among the F. oxysporum f. sp. cepae isolates were in the range of 14–85%. Cluster analysis, using the unweighted pair-group method with arithmetic average, clearly separated the isolates into two clusters (A and B) confirming the genetic diversity among the isolates of F. oxysporum f. sp. cepae from onion.